Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009504.1 Corchorus capsularis cultivar CVL-1 contig09525, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22737
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6504 original size:3 final size:3
Alignment explanation
Indices: 6496--6524 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6486 TATAGTATAG
6496 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6525 CTATATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7091 original size:3 final size:3
Alignment explanation
Indices: 7083--7108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7073 ATATATATAG
7083 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
7109 ACTATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11911 original size:11 final size:11
Alignment explanation
Indices: 11868--11905 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11858 TTCCTATATA
*
11868 AAATAAATTAT
1 AAATTAATTAT
11879 CAAA-TAATTAT
1 -AAATTAATTAT
11890 AAATTAATTAT
1 AAATTAATTAT
11901 AAATT
1 AAATT
11906 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:12290 original size:41 final size:42
Alignment explanation
Indices: 12218--12301 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
12208 CAAAAATTTC
12218 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
12260 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
12301 A
1 A
12302 CAGTCGCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 28 0.67
42 14 0.33
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:12922 original size:12 final size:12
Alignment explanation
Indices: 12905--12935 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12895 CCTTTAAGGA
12905 GCACCAAATTGG
1 GCACCAAATTGG
12917 GCACCAAATTGG
1 GCACCAAATTGG
12929 GC-CCAAA
1 GCACCAAA
12936 CGTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.13
Consensus pattern (12 bp):
GCACCAAATTGG
Found at i:13102 original size:15 final size:14
Alignment explanation
Indices: 13076--13119 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
13066 TCAACATTAA
13076 TTTCTATTTTTTCTT
1 TTTCT-TTTTTTCTT
*
13091 TTTACTTTTTTTCCT
1 TTT-CTTTTTTTCTT
*
13106 TTTCTTATTTTCTT
1 TTTCTTTTTTTCTT
13120 CTTTTACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 14 0.56
16 2 0.08
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:17502 original size:8 final size:8
Alignment explanation
Indices: 17485--17557 Score: 101
Period size: 8 Copynumber: 8.6 Consensus size: 8
17475 TAATGTAGGG
*
17485 TACATATA
1 TACATCTA
17493 TACATCTA
1 TACATCTA
17501 TACATATCTA
1 TAC--ATCTA
17511 TACATCTA
1 TACATCTA
17519 TACATCTA
1 TACATCTA
17527 TACATATCTA
1 TAC--ATCTA
17537 TACATCTA
1 TACATCTA
17545 TACATCTA
1 TACATCTA
17553 TACAT
1 TACAT
17558 GCATATATAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
8 44 0.73
10 16 0.27
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (8 bp):
TACATCTA
Found at i:17564 original size:18 final size:16
Alignment explanation
Indices: 17485--17557 Score: 101
Period size: 18 Copynumber: 4.3 Consensus size: 16
17475 TAATGTAGGG
*
17485 TACATATATACATCTA
1 TACATCTATACATCTA
17501 TACATATCTATACATCTA
1 TAC--ATCTATACATCTA
17519 TACATCTATACATATCTA
1 TACATCTATAC--ATCTA
17537 TACATCTATACATCTA
1 TACATCTATACATCTA
17553 TACAT
1 TACAT
17558 GCATATATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
16 21 0.40
18 31 0.60
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (16 bp):
TACATCTATACATCTA
Found at i:17564 original size:26 final size:26
Alignment explanation
Indices: 17485--17557 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
17475 TAATGTAGGG
*
17485 TACATATATACATCTATACATATCTA
1 TACATCTATACATCTATACATATCTA
17511 TACATCTATACATCTATACATATCTA
1 TACATCTATACATCTATACATATCTA
17537 TACATCTATACATCTATACAT
1 TACATCTATACATCTATACAT
17558 GCATATATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (26 bp):
TACATCTATACATCTATACATATCTA
Found at i:18275 original size:20 final size:20
Alignment explanation
Indices: 18226--18264 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
18216 GTTTGGTTTG
18226 AGGAGTTTGAAGGGGTGGGA
1 AGGAGTTTGAAGGGGTGGGA
18246 AGGAGTTTGAAGGGGTGGG
1 AGGAGTTTGAAGGGGTGGG
18265 TAATTGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.56, T:0.21
Consensus pattern (20 bp):
AGGAGTTTGAAGGGGTGGGA
Found at i:18410 original size:293 final size:293
Alignment explanation
Indices: 17883--18463 Score: 1081
Period size: 293 Copynumber: 2.0 Consensus size: 293
17873 ATATTAACTC
* *
17883 AATCTACTATTTGATTGGCTTTTTTTGTGATTTAGCCTTTGTTTGGTTTGGGGAGTTTGAAGGGG
1 AATCTACTATTTGATTGGCTTTTTTTGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGG
17948 TGGAAAGGAGTTTGAAGGGGTGGGTAATTGTTTGATTTAGGTAATAGGGAAGGATGAGGGGTAGG
66 TGGAAAGGAGTTTGAAGGGGTGGGTAATTGTTTGATTTAGGTAATAGGGAAGGATGAGGGGTAGG
* *
18013 AAGGGGTGGGTCCCACCCCTCTTAACCCTTATAATCCACCCCTCGAAATCGGGGTATTTGGGAGA
131 AAGGGGTAGGTCCCACCCCTCTAAACCCTTATAATCCACCCCTCGAAATCGGGGTATTTGGGAGA
18078 GGTGGATTTTAGACATAAAATTGGTTGACAAGATTAGTTCCATCACATTTTGTATAATCCCAAAT
196 GGTGGATTTTAGACATAAAATTGGTTGACAAGATTAGTTCCATCACATTTTGTATAATCCCAAAT
18143 TAGCCTAAAATATTTTTTTCCTTTGTTTTGTAT
261 TAGCCTAAAATATTTTTTTCCTTTGTTTTGTAT
*
18176 AATCTACTATTTGATTGTCTTTTTTTGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGG
1 AATCTACTATTTGATTGGCTTTTTTTGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGG
* *
18241 TGGGAAGGAGTTTGAAGGGGTGGGTAATTGTTTGATTTGGGTAATAGGGAAGGATGAGGGGTAGG
66 TGGAAAGGAGTTTGAAGGGGTGGGTAATTGTTTGATTTAGGTAATAGGGAAGGATGAGGGGTAGG
18306 AAGGGGTAGGTCCCACCCCTCTAAACCCTTATAATCCACCCCTCGAAATCGGGGTATTTGGGAGA
131 AAGGGGTAGGTCCCACCCCTCTAAACCCTTATAATCCACCCCTCGAAATCGGGGTATTTGGGAGA
* *
18371 GGTGTATTTTAGACATAAAATTGGTTGACGAGATTAGTTCCATCACATTTTGTATAATCCCAAAT
196 GGTGGATTTTAGACATAAAATTGGTTGACAAGATTAGTTCCATCACATTTTGTATAATCCCAAAT
18436 TAGCCTAAAATATTTTTTTCCTTTGTTT
261 TAGCCTAAAATATTTTTTTCCTTTGTTT
18464 GATAATAGCT
Statistics
Matches: 279, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
293 279 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (293 bp):
AATCTACTATTTGATTGGCTTTTTTTGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGG
TGGAAAGGAGTTTGAAGGGGTGGGTAATTGTTTGATTTAGGTAATAGGGAAGGATGAGGGGTAGG
AAGGGGTAGGTCCCACCCCTCTAAACCCTTATAATCCACCCCTCGAAATCGGGGTATTTGGGAGA
GGTGGATTTTAGACATAAAATTGGTTGACAAGATTAGTTCCATCACATTTTGTATAATCCCAAAT
TAGCCTAAAATATTTTTTTCCTTTGTTTTGTAT
Found at i:19243 original size:148 final size:149
Alignment explanation
Indices: 18975--19271 Score: 578
Period size: 148 Copynumber: 2.0 Consensus size: 149
18965 TACATCTATA
18975 CATACATATATAATTCCTTTGAAAATTACAATTTAACCCCTATTTAATCTAAATATATTAACTCA
1 CATACATATATAATTCCTTTGAAAATTACAATTTAACCCCTATTTAATCTAAATATATTAACTCA
19040 ATCTACTATTTGATTGGCTTTTTGGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGGT-
66 ATCTACTATTTGATTGGCTTTTTGGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGGTG
19104 GGTAATTGTTTGATTTGGG
131 GGTAATTGTTTGATTTGGG
19123 CATACATATATAATTCCTTTGAAAATTACAATTTAACCCCTATTTAATCTAAATATATTAACTCA
1 CATACATATATAATTCCTTTGAAAATTACAATTTAACCCCTATTTAATCTAAATATATTAACTCA
*
19188 ATCTACTATTTGATTGGCTTTTTGGTCATTTAGTCTTTGTTTGGTTTGAGGAGTTTGAAGGGGTG
66 ATCTACTATTTGATTGGCTTTTTGGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGGTG
19253 GGTAATTGTTTGATTTGGG
131 GGTAATTGTTTGATTTGGG
19272 TAACAGGGAA
Statistics
Matches: 147, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
148 128 0.87
149 19 0.13
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (149 bp):
CATACATATATAATTCCTTTGAAAATTACAATTTAACCCCTATTTAATCTAAATATATTAACTCA
ATCTACTATTTGATTGGCTTTTTGGTCATTTAGCCTTTGTTTGGTTTGAGGAGTTTGAAGGGGTG
GGTAATTGTTTGATTTGGG
Done.